rs3124955
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_004108.3(FCN2):c.214+60T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.353 in 1,207,266 control chromosomes in the GnomAD database, including 75,866 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.32 ( 8131 hom., cov: 32)
Exomes 𝑓: 0.36 ( 67735 hom. )
Consequence
FCN2
NM_004108.3 intron
NM_004108.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -3.19
Genes affected
FCN2 (HGNC:3624): (ficolin 2) The product of this gene belongs to the ficolin family of proteins. This family is characterized by the presence of a leader peptide, a short N-terminal segment, followed by a collagen-like region, and a C-terminal fibrinogen-like domain. This gene is predominantly expressed in the liver, and has been shown to have carbohydrate binding and opsonic activities. Alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.96).
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.42 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FCN2 | NM_004108.3 | c.214+60T>C | intron_variant | ENST00000291744.11 | |||
FCN2 | NM_015837.3 | c.101-603T>C | intron_variant | ||||
FCN2 | XM_006717015.5 | c.68-603T>C | intron_variant | ||||
FCN2 | XM_011518392.4 | c.181+60T>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FCN2 | ENST00000291744.11 | c.214+60T>C | intron_variant | 1 | NM_004108.3 | P1 | |||
FCN2 | ENST00000350339.3 | c.101-603T>C | intron_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.322 AC: 48825AN: 151768Hom.: 8123 Cov.: 32
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GnomAD4 exome AF: 0.357 AC: 377017AN: 1055380Hom.: 67735 AF XY: 0.360 AC XY: 194455AN XY: 540280
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GnomAD4 genome ? AF: 0.322 AC: 48837AN: 151886Hom.: 8131 Cov.: 32 AF XY: 0.322 AC XY: 23913AN XY: 74226
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at